This was Duterte's fifth visit to China in his three years in office, and his eighth meeting with Xi.
Duterte will discuss the South China Sea issue along with a 2016 ruling by an global court that rejected China's sweeping claims in the area, Salvador Panelo, Philippines presidential spokesman, told reporters before Duterte left for Beijing on Wednesday, according to the daily Manila Standard.
The two sides also signed a preliminary agreement last November that could open the way for joint oil and gas exploration in the South China Sea, long a hot button issue - many in the Philippines fear that agreeing to joint exploitation is tantamount to acknowledging the legitimacy of Chinese claims to resources that should be the Philippines' alone.
He had largely avoided the subject, opting instead to curry favour with China.
Mr. Duterte has sought warmer ties with Beijing and has always been criticized by nationalists and left-wing groups in the Philippines for not immediately demanding Chinese compliance with the ruling.
"He has decided that it's the time to include in the diplomatic agenda", said Santa Romana, adding "he's not coming here to provoke the Chinese".
Mr. Lopez said the Chinese President reiterated Beijing's policy to help balance trade with the Philippines "by buying more goods especially agriculture and agri-based products and industrial goods".
"This will only be the start of the process", Batongbacal said. "At best, Duterte might be seen as using the arbitration discussion as a move to leverage other concessions".
The meeting comes at a tense time between the two countries.
"This will not only benefit our two countries and our peoples, but also will provide positive energy to the region", Xi said.
Before he left for Beijing, Mr Duterte raised expectations on the matter, even though it was unclear what he sought to achieve by pressing the arbitration victory midway into his six-year term.
On Thursday, China and the Philippines announced the establishment of an "intergovernmental joint steering committee and a working group between relevant enterprises" on oil and gas cooperation, Xinhua reported.
The region became a flashpoint of ongoing tensions between China and the Philippines. Now under pressure to stand up for global rules about ownership and use of offshore waters, he is finally protesting China's affront to worldwide law.
China has said it is ready to work with the Philippines to jointly safeguard maritime security and order.
Nearly three months after a Chinese vessel rammed and sank a Filipino fishing boat, the vessel's owner has finally apologized at least by proxy.
"I feel deep regret that this accident had to happen and I would like to express my deep sympathy to the Filipino fishermen".
Duterte told Xi that the 2016 ruling of an worldwide arbitration panel in The Hague, in which China had refused to participate, "is final, binding and not subject to appeal".